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Annual rainfall averages only between 200 and 600 millimeters in the most arable portions of Libya. The Great Manmade River Project, designed to bring water from fossil aquifers beneath the Sahara, has no long-term viability because of the finite nature of the fossil reserves.
A major environmental concern in Libya is the depletion of underground water as a result of overuse in agricultural developments, causing salinity and sea-water penetration into the coastal aquifers. The Great Man-Made River Project, currently under development to transport water from large aquifers under the Sahara Desert to coastal cities, is the world's most extensive water supply project.

Another significant environmental problem in Libya is water pollution. The combined impact of sewage, oil byproducts, and industrial waste threatens Libya's coast and the Mediterranean Sea generally. Libya has 0.8 cu km of renewable water resources with 87% used in farming activity and 4% for industrial purposes. Only about 68% of the people living in rural areas have pure drinking water. Libya's cities produce about 0.6 million tons of solid waste per year. The desertification of existing fertile areas is being combated by the planting of trees as windbreaks.

As of 2001, 11 of Libya's mammal species and 2 of its bird species were endangered. About 41 of its plant species were also endangered. Endangered species in Libya include the Mediterranean monk seal, the leopard, and the slender-horned gazelle. The Bubal hartebeest and Sahara oryx are extinct.